I didn't know how to formulate my question, you will understand a lot better with some screenshots.
I'm currently saving my figure with:
That is a size problem, as the savefig instruction is saving it with a non suitable shape. In order to get a proper size, you have to set the figsize parameter to the one that fits your plot:
width = 18 height = 6 plt.figure(figsize=(width, height)) plt.savefig('test.pdf', bbox_inches='tight')